millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-12-22 10:38:16 +00:00
Code Issues Releases Packages Activity

Add emitting porechop logs to multiqc and fix collection of others

Browse source
This commit is contained in:
James Fellows Yates 2022-07-19 13:50:39 +02:00
parent 6f269a8245
commit 33a5402b25
7 changed files with 459 additions and 4 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

445
docs/images/nf-core-taxprofiler_icon_border.svg Normal file
View file

@ -0,0 +1,445 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Created with Inkscape (http://www.inkscape.org/) -->
<svg
width="180mm"
height="180mm"
viewBox="0 0 180 180"
version="1.1"
id="svg5581"
inkscape:version="1.2 (1:1.2+202206011327+fc4e4096c5)"
sodipodi:docname="nf-core-taxprofiler_icon_border.svg"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns="http://www.w3.org/2000/svg"
xmlns:svg="http://www.w3.org/2000/svg">
<sodipodi:namedview
id="namedview5583"
pagecolor="#ffffff"
bordercolor="#666666"
borderopacity="1.0"
inkscape:showpageshadow="2"
inkscape:pageopacity="0.0"
inkscape:pagecheckerboard="0"
inkscape:deskcolor="#d1d1d1"
inkscape:document-units="mm"
showgrid="true"
inkscape:zoom="0.41291035"
inkscape:cx="449.25006"
inkscape:cy="446.82823"
inkscape:window-width="1920"
inkscape:window-height="1016"
inkscape:window-x="784"
inkscape:window-y="1107"
inkscape:window-maximized="1"
inkscape:current-layer="layer1">
<inkscape:grid
type="xygrid"
id="grid6096"
originx="-7.7520638"
originy="-7.8991984"
dotted="true" />
</sodipodi:namedview>
<defs
id="defs5578">
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient30057"
x1="10.213824"
y1="221.42242"
x2="218.95003"
y2="221.42242"
gradientUnits="userSpaceOnUse"
gradientTransform="matrix(0.6691607,0.01747377,-0.01751914,0.67089835,5.6293239,-100.28017)" />
<linearGradient
x1="0"
y1="0"
x2="1"
y2="0"
gradientUnits="userSpaceOnUse"
gradientTransform="matrix(37.87862,-29.594021,-29.594021,-37.87862,275.46292,136.24821)"
spreadMethod="pad"
id="linearGradient21662">
<stop
style="stop-opacity:1;stop-color:#000000"
offset="0"
id="stop21652" />
<stop
style="stop-opacity:1;stop-color:#0c542a"
offset="0.214724"
id="stop21654" />
<stop
style="stop-opacity:1;stop-color:#25af64"
offset="0.84662598"
id="stop21656" />
<stop
style="stop-opacity:1;stop-color:#25af64"
offset="0.846626"
id="stop21658" />
<stop
style="stop-opacity:1;stop-color:#25af64"
offset="1"
id="stop21660" />
</linearGradient>
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient2708"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174"
gradientUnits="userSpaceOnUse" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6027"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6029"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6031"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6033"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6035"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6037"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6039"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6041"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6043"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6045"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6047"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6049"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6051"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6053"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6055"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6057"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6059"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6061"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6063"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6065"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6067"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
<linearGradient
inkscape:collect="always"
xlink:href="#linearGradient21662"
id="linearGradient6069"
gradientUnits="userSpaceOnUse"
x1="14.381735"
y1="80.392174"
x2="49.04929"
y2="80.392174" />
</defs>
<g
inkscape:label="Layer 1"
inkscape:groupmode="layer"
id="layer1"
transform="translate(-7.7520638,-7.8991986)">
<g
id="g6123"
transform="translate(17.317549,39.640907)">
<path
id="path30012-5"
style="fill:#ffffff;fill-opacity:1;stroke:none;stroke-width:0.424868;stroke-linecap:round"
d="M 9.5900834,8.8480637 C 7.5556439,12.028833 7.7408039,16.123943 7.7687039,19.769833 c 0.83412,6.65305 4.1623501,13.08043 9.6588001,17.05639 2.95411,2.45491 6.166,4.56934 9.30414,6.77667 -1.90794,4.17676 -2.98236,9.29825 -0.29786,13.40918 1.67713,3.72229 4.84583,6.89989 5.31985,11.06218 -0.73221,2.86643 -3.54676,6.3663 -0.97712,9.12477 2.12262,2.77099 4.06395,5.64907 5.35322,8.82231 2.02674,3.35439 6.5976,4.09759 10.20366,3.73748 2.47738,-0.18007 4.72202,-2.67715 3.28025,-5.08004 -1.18247,-2.55998 -4.28744,-2.18411 -6.38635,-3.25125 -1.36801,-2.44734 -3.00653,-5.99123 -0.26124,-8.17889 2.5926,-2.70872 4.69882,-5.81991 6.94515,-8.77398 2.71899,-1.24434 5.98816,-0.0654 8.84595,0.2859 10.88656,2.48435 21.31368,6.88721 32.36055,8.64773 3.13924,0.41138 6.76175,-0.45373 9.579516,0.92166 1.40942,4.43747 2.34224,9.45414 5.76225,12.84528 2.6934,1.93573 7.02228,2.12481 9.53599,-0.13787 1.60636,-2.93172 -1.52253,-5.89536 -4.20194,-6.62585 -0.40071,-2.8223 -0.37969,-5.87179 0.26854,-8.58529 3.77785,-0.24182 7.24094,1.16954 10.61732,2.45295 1.78619,3.3965 5.12259,5.96321 8.91186,6.64761 1.60415,-1.40492 2.56073,1.72858 3.8909,2.50862 2.79709,2.93023 6.8997,5.0038 10.99366,4.75587 3.26301,-0.67749 3.79546,-4.59452 2.47471,-7.17014 -0.80988,-4.2018 -3.22071,-8.59389 -1.2047,-12.82352 1.17357,-5.20598 -1.35199,-10.96325 -5.77146,-13.90702 -4.33733,-3.64436 -10.39077,-3.64653 -14.92742,-6.93614 -10.03223,-6.15469 -21.64077,-9.58338 -33.280326,-11.28456 -12.56653,-0.98847 -25.20371,-0.69003 -37.78225,-1.58411 -7.09295,-0.25502 -14.55087,-1.15633 -21.23347,1.84537 -3.9067,-0.36049 -7.22928,-2.98747 -10.60062,-4.8325 -3.63865,-2.26998 -7.6488,-4.94361 -8.46777,-9.49866 -1.63814,-4.07488 -1.20485,-8.6292 -2.57509,-12.7242393 -0.092,-1.43702 -3.1468606,-2.01015 -3.5173206,-0.42766 z" />
<path
style="fill:url(#linearGradient30057);fill-opacity:1;stroke:none;stroke-width:0.424868;stroke-linecap:round"
d="M 10.931314,9.9653233 C 9.7827934,11.308473 9.8484234,13.338583 9.5801634,15.027613 c -0.34115,2.76171 -0.29206,5.58762 0.6731896,8.22888 1.139301,3.87108 2.982591,7.65359 6.139101,10.27078 3.79198,3.54184 8.2401,6.33641 12.43029,9.30118 -0.91535,2.99306 -2.65543,5.87431 -2.30804,9.13471 0.18061,2.677 1.94571,4.91009 3.11856,7.23201 1.50937,2.8256 3.84729,5.54985 3.82514,8.91032 -0.0787,2.49314 -2.48083,4.5082 -1.96562,7.03872 1.67419,2.68138 3.992,4.96942 5.15932,7.96769 0.65556,1.60629 1.4695,3.40539 3.31812,3.87174 2.38126,0.82152 5.41091,1.64045 7.63103,0.0125 0.82635,-1.48261 -1.06902,-2.72955 -2.36736,-2.87342 -1.71199,-0.17589 -3.69466,-0.59568 -4.39228,-2.41244 -0.96281,-2.26721 -2.29358,-4.88743 -1.3576,-7.36922 2.00069,-3.29907 5.15025,-5.72284 7.05316,-9.10416 0.97281,-1.66962 2.43831,-3.35242 4.55042,-3.26353 6.66383,-0.13609 13.02922,2.25844 19.35504,4.0482 6.38637,1.7963 12.67764,4.02096 19.20445,5.25889 3.77887,0.58276 7.72718,-0.18602 11.419706,0.93529 1.63461,0.75428 1.35512,2.9334 2.05535,4.34159 1.1597,3.06423 1.81242,6.5515 4.16823,8.9707 1.76834,1.42588 4.39281,1.36118 6.4399,0.63293 1.20689,-0.70879 -0.0705,-2.295 -0.82735,-2.84018 -0.85353,-0.97431 -2.49109,-0.81793 -3.19991,-1.88904 -0.61703,-3.21399 -0.48223,-6.57875 0.0181,-9.80404 0.2319,-1.63989 2.04068,-2.10159 3.44204,-1.83986 3.30625,0.10127 6.50718,1.46919 9.55674,2.3424 -0.71254,-1.81326 -1.19119,-3.75193 -0.97348,-5.72815 0.0204,-1.69846 0.15688,-3.58482 1.5917,-4.73058 1.83011,-1.86627 3.60232,-3.85815 5.70315,-5.41088 0.57552,0.16274 -0.36083,0.85452 -0.4987,1.09386 -1.90807,2.09201 -4.24787,3.84191 -5.83093,6.20217 -0.46736,1.92903 -0.41493,3.99677 -0.24575,5.96645 0.84833,2.57726 2.1706,5.12487 4.1346,7.01585 1.36224,0.87656 2.75795,2.00764 4.37729,2.2713 1.6213,-0.74843 1.95011,-2.85006 2.55124,-4.35962 1.10913,-3.99969 1.90782,-8.08534 2.71945,-12.15319 0.1702,-1.75995 0.75519,-4.04477 -0.9398,-5.26766 -0.66443,-0.31636 -0.15084,-1.05324 0.36147,-0.52827 2.02638,1.51086 1.30614,4.35901 1.06011,6.49585 -0.85333,4.26646 -1.66477,8.56551 -2.96213,12.72302 -0.11797,0.91577 -1.34029,1.9982 -0.53389,2.72401 2.58751,2.57362 4.81242,5.92113 8.5085,6.96547 1.59827,0.50471 3.80045,1.66945 5.18808,0.14586 1.17766,-1.4017 -0.0976,-3.1877 -0.28432,-4.72092 -0.75396,-3.29433 -2.15674,-6.56045 -1.96438,-9.99106 0.37367,-2.10533 1.65495,-4.11536 1.02167,-6.32262 -0.34992,-2.84568 -1.45335,-5.69952 -3.77909,-7.50012 -2.77154,-2.67603 -6.40479,-4.14933 -10.09936,-5.01092 -3.81561,-1.24593 -6.9919,-3.83431 -10.61749,-5.50364 -6.72466,-3.69962 -14.2084,-5.65169 -21.615834,-7.44474 -8.303242,-1.93229 -16.888842,-1.47941 -25.343602,-1.84797 -8.46313,-0.1352 -16.90366,-0.80082 -25.3617,-1.05107 -4.38737,-0.20312 -8.92121,-0.0523 -12.99753,1.77349 -2.83378,1.235 -5.55113,-0.83445 -8.06653,-1.90121 -3.95435,-2.11512 -8.20653,-4.63235 -11.45036,-7.81607 -1.44093,-1.52832 -1.98381,-3.13498 -2.61394,-4.93556 -0.98461,-2.81345 -1.62386,-5.97312 -1.9462,-9.06999 -0.24149,-1.39646 -0.0764,-3.01443 -0.81326,-4.2426397 -0.0219,-0.007 -0.045,-0.0107 -0.0678,-0.007 z"
id="path30012"
sodipodi:nodetypes="cccccccccccccccccccccccccccccccccccccccccccccccccccccccccscccc"
inkscape:export-filename="/Users/whx424/Pictures/Illustrations/taxprofiler_v11.png"
inkscape:export-xdpi="159"
inkscape:export-ydpi="159" />
<path
id="path1218-5-4"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 36.798094,98.985353 a 7.0058785,6.6371479 0 0 1 -7.00588,6.637147 7.0058785,6.6371479 0 0 1 -7.00589,-6.637147 7.0058785,6.6371479 0 0 1 7.00589,-6.63713 7.0058785,6.6371479 0 0 1 7.00588,6.63713 z" />
<path
id="path1218-8-0"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 48.458974,96.857863 a 7.0058789,6.6371479 0 0 1 -7.00588,6.637147 7.0058789,6.6371479 0 0 1 -7.00588,-6.637147 7.0058789,6.6371479 0 0 1 7.00588,-6.63715 7.0058789,6.6371479 0 0 1 7.00588,6.63715 z" />
<path
id="path1218-4-46"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 59.481564,99.639333 a 7.0058789,6.6371479 0 0 1 -7.00588,6.637157 7.0058789,6.6371479 0 0 1 -7.00588,-6.637157 7.0058789,6.6371479 0 0 1 7.00588,-6.63715 7.0058789,6.6371479 0 0 1 7.00588,6.63715 z" />
<path
id="path1218-7-4"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 71.168234,96.889183 a 7.0058785,6.6371479 0 0 1 -7.00589,6.637157 7.0058785,6.6371479 0 0 1 -7.00588,-6.637157 7.0058785,6.6371479 0 0 1 7.00588,-6.63715 7.0058785,6.6371479 0 0 1 7.00589,6.63715 z" />
<path
id="path1218-1-6"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 82.714904,99.255233 a 7.0058789,6.6371479 0 0 1 -7.00587,6.637147 7.0058789,6.6371479 0 0 1 -7.00588,-6.637147 7.0058789,6.6371479 0 0 1 7.00588,-6.63714 7.0058789,6.6371479 0 0 1 7.00587,6.63714 z" />
<path
id="path1218-73-4"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 93.813184,96.584163 a 7.0058789,6.6371479 0 0 1 -7.00588,6.637147 7.0058789,6.6371479 0 0 1 -7.00587,-6.637147 7.0058789,6.6371479 0 0 1 7.00587,-6.63715 7.0058789,6.6371479 0 0 1 7.00588,6.63715 z" />
<path
id="path1218-5-9-3"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 104.85924,98.601273 a 7.0058789,6.6371479 0 0 1 -7.005886,6.637147 7.0058789,6.6371479 0 0 1 -7.00588,-6.637147 7.0058789,6.6371479 0 0 1 7.00588,-6.63716 7.0058789,6.6371479 0 0 1 7.005886,6.63716 z" />
<path
id="path1218-8-7-8"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 116.52015,96.473773 a 7.0058785,6.6371479 0 0 1 -7.00589,6.637127 7.0058785,6.6371479 0 0 1 -7.00588,-6.637127 7.0058785,6.6371479 0 0 1 7.00588,-6.63714 7.0058785,6.6371479 0 0 1 7.00589,6.63714 z" />
<path
id="path1218-4-7-4"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 127.54274,99.255233 a 7.0058789,6.6371479 0 0 1 -7.00589,6.637147 7.0058789,6.6371479 0 0 1 -7.00588,-6.637147 7.0058789,6.6371479 0 0 1 7.00588,-6.63714 7.0058789,6.6371479 0 0 1 7.00589,6.63714 z" />
<path
id="path1218-7-9-00"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 139.22941,96.505103 a 7.0058785,6.6371479 0 0 1 -7.00587,6.637147 7.0058785,6.6371479 0 0 1 -7.00588,-6.637147 7.0058785,6.6371479 0 0 1 7.00588,-6.63716 7.0058785,6.6371479 0 0 1 7.00587,6.63716 z" />
<path
id="path1218-1-5-9"
style="fill:#ffffff;fill-opacity:1;stroke:#ffffff;stroke-width:4.68179;stroke-linecap:round"
d="m 150.77607,98.871153 a 7.0058785,6.6371479 0 0 1 -7.00588,6.637137 7.0058785,6.6371479 0 0 1 -7.00588,-6.637137 7.0058785,6.6371479 0 0 1 7.00588,-6.63715 7.0058785,6.6371479 0 0 1 7.00588,6.63715 z" />
<g
id="g2682"
style="fill:url(#linearGradient2708);fill-opacity:1;stroke:url(#linearGradient2708)"
inkscape:export-filename="/Users/whx424/Pictures/Illustrations/taxprofiler_v11.png"
inkscape:export-xdpi="159"
inkscape:export-ydpi="159"
transform="matrix(3.7156967,0,0,3.7156967,-30.828156,-200.55501)">
<ellipse
style="fill:url(#linearGradient6027);fill-opacity:1;stroke:url(#linearGradient6029);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-5"
cx="16.378149"
cy="80.642143"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6031);fill-opacity:1;stroke:url(#linearGradient6033);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-8"
cx="19.516428"
cy="80.069572"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6035);fill-opacity:1;stroke:url(#linearGradient6037);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-4"
cx="22.48292"
cy="80.818146"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6039);fill-opacity:1;stroke:url(#linearGradient6041);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-7"
cx="25.628136"
cy="80.078003"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6043);fill-opacity:1;stroke:url(#linearGradient6045);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-1"
cx="28.735676"
cy="80.714775"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6047);fill-opacity:1;stroke:url(#linearGradient6049);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-73"
cx="31.72254"
cy="79.995911"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6051);fill-opacity:1;stroke:url(#linearGradient6053);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-5-9"
cx="34.695347"
cy="80.538773"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6055);fill-opacity:1;stroke:url(#linearGradient6057);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-8-7"
cx="37.83363"
cy="79.966202"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6059);fill-opacity:1;stroke:url(#linearGradient6061);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-4-7"
cx="40.800121"
cy="80.714775"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6063);fill-opacity:1;stroke:url(#linearGradient6065);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-7-9"
cx="43.945339"
cy="79.974632"
rx="1.4964142"
ry="1.4176555" />
<ellipse
style="fill:url(#linearGradient6067);fill-opacity:1;stroke:url(#linearGradient6069);stroke-width:1;stroke-linecap:round;stroke-miterlimit:4;stroke-dasharray:none"
id="path1218-1-5"
cx="47.052876"
cy="80.611404"
rx="1.4964142"
ry="1.4176555" />
</g>
</g>
</g>
</svg>
Side by side

After

Width:  |  Height:  |  Size: 22 KiB

BIN
docs/images/nf_core_taxprofiler_icon_border.png Normal file
View file

Binary file not shown.
Side by side

After

Width:  |  Height:  |  Size: 139 KiB

2
modules.json
View file

@ -88,7 +88,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"porechop": {
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
"git_sha": "b78e19b9dae3671db2c7d4346fe04452c1debfab"
},
"prinseqplusplus": {
"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"

4
modules/nf-core/modules/porechop/main.nf generated
View file

@ -12,6 +12,7 @@ process PORECHOP {
output:
tuple val(meta), path("*.fastq.gz"), emit: reads
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
@ -25,7 +26,8 @@ process PORECHOP {
-i $reads \\
-t $task.cpus \\
$args \\
-o ${prefix}.fastq.gz
-o ${prefix}.fastq.gz \\
> ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":

5
modules/nf-core/modules/porechop/meta.yml generated
View file

@ -38,6 +38,10 @@ output:
type: file
description: Demultiplexed and/or adapter-trimmed fastq.gz file
pattern: "*.{fastq.gz}"
- log:
type: file
description: Log file containing stdout information
pattern: "*.log"
authors:
- "@ggabernet"
@ -48,3 +52,4 @@ authors:
- "@jonasscheid"
- "@jonoave"
- "@GokceOGUZ"
- "@jfy133"

5
subworkflows/local/longread_preprocessing.nf
View file

@ -23,9 +23,11 @@ workflow LONGREAD_PREPROCESSING {
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
}
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log.collect{it[1]}.ifEmpty([]) )
} else if ( !params.longread_qc_run_clip && params.longread_qc_run_filter ) {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
@ -45,6 +47,7 @@ workflow LONGREAD_PREPROCESSING {
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log.collect{it[1]}.ifEmpty([]) )
}

2
subworkflows/local/profiling.nf
View file

@ -227,7 +227,7 @@ workflow PROFILING {
MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.collect{it[1]}.ifEmpty([]) )
}
emit: